Block specific information at item description page

[David Da Silva Pires]

Hello!

Some years ago I had configured a BED track such that when you click on a block (exon), the item page was loaded and it was showed a content specific for that item. I don't remember how I did that and now I have to implement the same thing again. The only thing that I remember is that I had to put a dollar sign ("$") at some field at trackDb.txt file, in order to differentiate the many pages that should be written, one for each item.

Can you, please, direct me to a help page that describes how can I do that?

By the way, I think that I learned about this technique at the wiki pages, but I was unable to find them now. Were they deleted? If so, why?

I'm very grateful for any help. Thanks in advance.

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David da Silva Pires

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[Gerardo Perez]

Hello, David.

Thank you for using the UCSC Genome Browser and for sending your inquiry.

Are you referring to a third-party page or a UCSC-hosted page that appears when clicking on an item in the Genome Browser graphic display?

It is possible you are referring to the directUrl setting. This setting allows items shown in the Genome Browser to link directly to a URL that can include the item name. For example:

directUrl http://mygenes.org/cgi-bin/geneView/%s

In this example, %s is replaced with the item name.

More information about using the directUrl setting is available here: https://genome.ucsc.edu/goldenPath/help/trackDb/trackDbHub.html#directUrl

We are not sure which wiki page you are referring to. If you remember the name of the page or some of its content, we would be happy to help track it down.

I hope this is helpful. Please include gen...@soe.ucsc.edu in any replies to ensure visibility by the team. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Gerardo Perez
UCSC Genomics Institute

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[David Da Silva Pires]

Hi Gerardo.

I'm interested in configuring a track hub that provides this feature.

You're right: the setting that I want is directUrl. It was an 's', not a '$'.   :-)   Thank you for redirecting me to its help page.

While searching for the solution, I found a blog post about showing information specific to an item while mouse hovering. A great solution for the same problem in my case.

Relative to the wiki page, I can't find any of them, not a specific one. It seems that the link for the wiki pages was deleted from the help menu.   :-(

Thanks again for your help.

Best regards.

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DAVID DA SILVA PIRES Especialista de Laboratório Laboratório de Ciclo Celular Tel: +55 11 2627-9734 fundacaobutantan.org.br

[Gerardo Perez]

Hello, David.

Thank you for following up with us.

We have moved the important information from the Genome Wiki to our main site at genome.ucsc.edu, and as part of that change, we also removed the Genomewiki link from the Help menu.

Could you let us know which specific Genome Wiki pages you found helpful? We would like to make sure that the same information is available in our current help documentation.

I hope this is helpful. Please include gen...@soe.ucsc.edu in any replies to ensure visibility by the team. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Gerardo Perez
UCSC Genomics Institute

On Wed, Apr 23, 2025 at 4:59 AM David Da Silva Pires <david...@fundacaobutantan.org.br> wrote:

Hi Gerardo.

I found the Wiki page:

https://genomewiki.ucsc.edu/index.php?title=Main_Page

It is very useful for me. Why was it removed from the Help menu?

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DAVID DA SILVA PIRES Especialista de Laboratório Laboratório de Ciclo Celular Tel: +55 11 2627-9734 fundacaobutantan.org.br

[David Da Silva Pires]

Hello, Gerardo.

The Genome Wiki page that is most helpful for me is one that I wrote myself:

https://genomewiki.ucsc.edu/index.php?title=GBiB:_From_download_to_BLAT_at_assembly_hubs

Although it is incomplete and a little mess (mainly at the final), it is very helpful when I have to:

• Install and maintain Genome Browser in a Box in a new virtual machine using VirtualBox.
• Configure a new assembly hub.
• Configure new track hubs, including the following tracks:
• Assembly.
• Gap.
• GC contents, using the command hgGcPercent.
• Blat and transBlat configuration, including the configuration of cron to start the Blat server as soon as the machine is turned on.
• A variety of tips, like:
• Use of the string "udcTimeout=1" at URL to get instant updates when changing configuration files.
• Setting of environment variables related to locale, in order to have a case-sensitive sort, which is necessary to use Kent's tools, like bedToBigBed.

The page deals with situations that I commonly find while configuring a new assembly or track hub, such as genome FASTA files with all the nucleotides with uppercase letters, very long chromosome names and the creation of the AGP file (used to create the assembly track). Besides that, sometimes I learnt a lot just by searching the topics written by other users (which is the idea of a wiki), mainly the ones related to automation using scripts in Bash. Some topics aren't directly related to UCSC Genome Browser, but concerning other topics that I consider very important while installing, configuring or using it.

I would love to have a list of the current help documentation pages that contain all the information described above. Yet, it is very comfortable for me to have all information related to a new assembly hub (with track hubs and Blat) all included in just one page. Do you think there is a similar page that could substitute the one that I wrote?

Best regards.

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DAVID DA SILVA PIRES Especialista de Laboratório Laboratório de Ciclo Celular Tel: +55 11 2627-9734 fundacaobutantan.org.br

[Clay Fischer]

Dear David,

Thank you for editing that wiki page and your question about similar resources. At this time we do not have an analogous documentation page.

We have been internally discussing how we might better organize our documentation, and are including your suggestions in our conversations. We will let you know if we find a solution that would be useful to you.

Thanks
Clay Fischer
UCSC Genomics Institute

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[David Da Silva Pires]

Hi Clay.

Thank you for dealing with this issue.

I can only imagine how difficult it is to manage the documentation for such a huge collection of tools and software like UCSC Genome Browser and Kent's tools. All of you do a great job and it is fantastic to know that you intend to make everything even better.

Thank you very much.

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DAVID DA SILVA PIRES Especialista de Laboratório Laboratório de Ciclo Celular Tel: +55 11 2627-9734 fundacaobutantan.org.br